Root exudates mediate plant defense against foliar pathogens by recruiting beneficial microbes

Highlights

•Ÿ Long-chain fatty acids and amino acids application could form foliar disease resistant-soil microbial community

•Ÿ Population of Pseudomonas was enriched by long-chain fatty acids and amino acids application

•Ÿ The enriched Pseudomonas could help plant resistant foliar pathogens.

Abstract

Plants are capable of releasing specific root exudates to recruit beneficial rhizosphere microbes upon foliar pathogen invasion attack, including long-chain fatty acids, amino acids, short-chain organic acids and sugars. Although long-chain fatty acids and amino acids application have been linked to soil legacy effects that improve future plant performance in the presence of the pathogen, the precise mechanisms involved are to a large extent still unknown. Here, we conditioned soils with long-chain fatty acids and amino acids application (L+ A) or short-chain organic acids and sugars (S+ S) to examine the direct role of such exudates on soil microbiome structure and function. The L+ A treatment recruited higher abundances of Proteobacteria which were further identified as members of the genera Sphingomonas, Pseudomonas, Roseiflexus, and Flavitalea. We then isolated the enriched bacterial strains from these groups, identifying ten Pseudomonas strains that were able to help host plant to resist foliar pathogen infection. Further investigation showed that the L+ A treatment resulted in growth promotion of these Pseudomonas strains. Collectively, our data suggest that long-chain fatty acids and amino acids stimulated by foliar pathogen infection can recruit specific Pseudomonas populations that can help protect the host plant or future plant generations.

Graphical abstract

Keywords

Foliar pathogen resistance / Pseudomonas / Recruitment / Root exudates

References

[1] Adler, J., 1973. A method for measuring chemotaxis and use of the method to determine optimum conditions for chemotaxis by Escherichia coli. Journal of General Microbiology 74, 77–91

[2] Bardgett, R.D., Wardle, D.A., (2010). Aboveground-Belowground Linkages: Biotic Interactions, Ecosystem Processes, And Global Change. Oxford University Press.

[3] Badri, D.V. Quintana N., El Kassis, E.G., Kim, H.K., Choi Y.H., Sugiyama, A., Verpoorte, R., Martinoia, E., Manter, D.K., Vivanco, J.M., 2009. An ABC transporter mutation alters root exudation of phytochemicals that provoke an overhaul of natural soil microbiota. Plant Physiol 151, 2006–2017

[4] Callahan, B.J., McMurdie, P.J., Rosen, M.J., Han, A.W., Johnson, A.J.A., Holmes, S.P., 2016. DADA2: high-resolution sample inference from Illumina amplicon data. Nature Methods 13, 581–583

[5] Edgar, R.C., 2016. UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. bioRxiv, doi: https://doi.org/10.1101/081257.

[6] Goodman, A.L., Kallstrom, G., Faith, J.J., Reyes, A., Moore, A., Dantas, G., Gordon, J.I., 2011. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proceedings of the National Academy of Sciences of the United States of America 108, 6252–6257

[7] Grigulis, K., Lavorel, S., Krainer, U., Legay, N., Baxendale, C., Dumont, M., Kastl, E., Arnoldi, C., Bardgett, R.D., Poly, F., Pommier, T., Schloter, M., Tappeiner, U., Bahn, M., Clément, J.C., 2013. Relative contributions of plant traits and soil microbial properties to mountain grassland ecosystem services. Journal of Ecology 101, 47–57

[8] Haney, C.H., Wiesmann, C.L., Shapiro, L.R., Melnyk, R.A., O’Sullivan, L.R., Khorasani, S., Xiao, L., Han, J., Bush, J., Carrillo, J., Pierce, N.E., Ausubel, F.M., 2018. Rhizosphere-associated Pseudomonas induce systemic resistance to herbivores at the cost of susceptibility to bacterial pathogens. Molecular Ecology 27, 1833–1847

[9] Höfle, M.G., Flavier, S., Christen, R., Bötel, J., Labrenz, M., Brettar, I., 2005. Retrieval of nearly complete 16S rRNA gene sequences from environmental DNA following 16S rRNA-based community fingerprinting. Environmental Microbiology 7, 670–675

[10] Huang, A.C., Jiang, T., Liu, Y., Bai, Y.C., Reed, J., Qu, B., Goossens, A., Nützmann, H.W., Bai, Y., Osbourn, A., 2019b. A specialized metabolic network selectively modulates Arabidopsis root microbiota. Science 364, 364

[11] Huang, A.C., Jiang, T., Liu, Y.-X., Bai, Y.-C., Reed, J., Qu, B.,Goossens, A., Nützmann, H.W., Bai, Y., Osbourn, A., 2019a. A specialized metabolic network selectively modulates Arabidopsis root microbiota. Science, 364, eaau6389.

[12] Kessler, A., Baldwin, I.T., 2001. Defensive function of herbivore-induced plant volatile emissions in nature. Science 291, 2141–2144

[13] Kessler, A., Baldwin, I.T., 2002. Plant responses to insect herbivory: the emerging molecular analysis. Annual Review of Plant Biology 53, 299–328

[14] Kim, S.J., Chun, J., Bae, K.S., Kim, Y.C., 2000. Polyphasic assignment of an aromatic-degrading Pseudomonas sp., strain DJ77, in the genus Sphingomonas as Sphingomonas chungbukensis sp. nov. International Journal of Systematic and Evolutionary Microbiology 50, 1641–1647

[15] Laughlin, D.C., 2011. Nitrification is linked to dominant leaf traits rather than functional diversity. Journal of Ecology 99, 1091–1099

[16] Love, M.I., Huber, W., Anders, S., 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15, 550

[17] Orwin, K.H., Buckland, S.M., Johnson, D., Turner, B.L., Smart, S., Oakley, S., Bardgett, R.D., 2010. Linkages of plant traits to soil properties and the functioning of temperate grassland. Journal of Ecology 98, 1074–1083

[18] Pieterse, C.M., Zamioudis, C., Berendsen, R.L., Weller, D.M., Van Wees, S.C., Bakker, P.A., 2014. Induced systemic resistance by beneficial microbes. Annual Review of Phytopathology 52, 347–375

[19] Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., Glöckner, F.O., 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41, D590–D596

[20] Rasmann, S., Köllner, T.G., Degenhardt, J., Hiltpold, I., Toepfer, S., Kuhlmann, U., Gershenzon, J., Turlings, T.C.J., 2005. Recruitment of entomopathogenic nematodes by insect-damaged maize roots. Nature 434, 732–737

[21] Ravanbakhsh, M., Kowalchuk, G.A., Jousset, A., 2019. Root-associated microorganisms reprogram plant life history along the growth–stress resistance tradeoff. ISME Journal 13, 3093–3101

[22] Rocelle, M., Clavero, S., Beuchat, L.R., 1995. Suitability of selective plating media for recovering heat- or freeze-stressed Escherichia coli O157: H7 from tryptic soy broth and ground beef. Applied and Environmental Microbiology 61, 3268–3273

[23] Rudrappa, T., Czymmek, K.J., Pare, P.W., Bais, H.P., 2008. Root-secreted malic acid recruits beneficial soil bacteria. Plant Physiology 148, 1547–1556

[24] Thompson, L.R., Sanders, J.G., McDonald, D., Amir, A., Ladau, J., Locey, K.J., Prill, R.J., Tripathi, A., Gibbons, S.M., Ackermann, G., Navas-Molina, J.A., Janssen, S., Kopylova, E., Vázquez-Baeza, Y., González, A., Morton, J.T., Mirarab, S., Zech Xu, Z., Jiang, L., Haroon, M.F., Kanbar, J., Zhu, Q., Jin Song, S., Kosciolek, T., Bokulich, N.A., Lefler, J., Brislawn, C.J., Humphrey, G., Owens, S.M., Hampton-Marcell, J., Berg-Lyons, D., McKenzie, V., Fierer, N., Fuhrman, J.A., Clauset, A., Stevens, R.L., Shade, A., Pollard, K.S., Goodwin, K.D., Jansson, J.K., Gilbert, J.A., Knight, R., 2017. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457–463

[25] Toju, H., Peay, K.G., Yamamichi, M., Narisawa, K., Hiruma, K., Naito, K., Fukuda, S., Ushio, M., Nakaoka, S., Onoda, Y., Yoshida, K., Schlaeppi, K., Bai, Y., Sugiura, R., Ichihashi, Y., Minamisawa, K., Kiers, E.T., 2018. Core microbiomes for sustainable agroecosystems. Nature Plants 4, 247–257

[26] Van Poecke, R.M., Posthumus, M.A., Dicke, M., 2001. Herbivore-induced volatile production by Arabidopsis thaliana leads to attraction of the parasitoid Cotesia rubecula: chemical, behavioral, and gene-expression analysis. Journal of Chemical Ecology 27, 1911–1928

[27] Vries, F.T., Manning, P., Tallowin, J.R., Mortimer, S.R., Pilgrim, E.S., Harrison, K.A., Hobbs, P.J., Quirk, H., Shipley, B., Cornelissen, J.H.C., Kattge, J., Bardgett, R.D., 2012. Abiotic drivers and plant traits explain landscape-scale patterns in soil microbial communities. Ecology Letters 15, 1230–1239

[28] Weller, D.M., Landa, B., Mavrodi, O., Schroeder, K., De La Fuente, L., Bankhead, S.B., Molar, R.A., Bonsall, R.F., Mavrodi, D.V., Thomashow, L.S., 2007. Role of 2, 4-diacetylphloroglucinol-producing fluorescent Pseudomonas spp. in the defense of plant roots. Plant Biology 9, 4–20

[29] Weller, D.M., Raaijmakers, J.M., Gardener, B.B., Thomashow, L.S., 2002. Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annual Review of Phytopathology 40, 309–348

[30] Yuan, J., Zhang, N., Huang, Q., Raza, W., Li, R., Vivanco, J.M., Shen, Q., 2015. Organic acids from root exudates of banana help root colonization of PGPR strain Bacillus amyloliquefaciens NJN-6. Scientific Reports 5, 13438

[31] Yuan, J., Zhao, J., Wen, T., Zhao, M., Li, R., Goossens, P., Huang, Q., Bai, Y., Vivanco, J.M., Kowalchuk, G.A., Berendsen, R.L., Shen, Q., 2018. Root exudates drive the soil-borne legacy of aboveground pathogen infection. Microbiome 6, 156

Competing interests

The authors declare that they have no competing interests.

Acknowledgments

We thank Ryan Penton (Arizona State University) for the comments on this manuscript. J. Y. was supported by the National Natural Science Foundation of China (31902107), Natural Science Foundation of Jiangsu Province (BK20170724), and National Postdoctoral Program for Innovative Talents (BX201600075).

Availability of data and materials

Sequence data are deposited in the NCBI Sequence Read Archive (SRA) database (SRP243322).

Authors’ contributions

JY: performed all experiments; JY and QS designed the study, and wrote the majority of the manuscript; JY, TW and MZ: analyzed the data; GAK: participated in the design of the study, provided comments and edited the manuscript.

RIGHTS & PERMISSIONS

2020 Higher Education Press